GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malF in Psychromonas ossibalaenae JAMM 0738

Align ABC-type maltose transporter (subunit 1/3) (EC 7.5.2.1) (characterized)
to candidate WP_051090303.1 G327_RS0109010 maltose ABC transporter permease MalF

Query= BRENDA::P02916
         (514 letters)



>NCBI__GCF_000381745.1:WP_051090303.1
          Length = 523

 Score =  585 bits (1508), Expect = e-171
 Identities = 289/499 (57%), Positives = 377/499 (75%), Gaps = 4/499 (0%)

Query: 15  LKWSVLGLLGLLVGYLVVLMYAQGEYLFAITTLILSSAGLYIFANRKAYAWRYVYPGMAG 74
           +KW +L L+ L  GY ++LMYAQ E +FA+ TL+L ++G+ +FA    Y+ RY+YPG+A 
Sbjct: 22  IKWGLLTLISLSAGYAIMLMYAQDEPVFAMLTLVLVASGVVVFARTDTYSHRYIYPGVAA 81

Query: 75  MGLFVLFPLVCTIAIAFTNYSSTNQLTFERAQEVLLDRSWQA-GKTYNFGLYPAGDEWQL 133
           + LF++FPL+ T+ IAFTNYS +NQLTFER Q   L ++++     Y F +Y   ++ ++
Sbjct: 82  IFLFIIFPLMYTVGIAFTNYSGSNQLTFERVQSQFLAQNYEKPDSAYKFDVYQLDND-KI 140

Query: 134 ALSDGETGKNYLSDAFKFG-GEQKLQLKETTAQPEGERANLRVITQNRQALSDITAILPD 192
            L   + G+ +++           + L  +TA  +GE+  +R + +NR+ALS +      
Sbjct: 141 QLHFSKDGEEFVTPEITLDQNNNNIALTPSTAAMQGEKVKIRFLVKNREALSKLAIQTVS 200

Query: 193 GNKVMMSSLRQFSGTQPLYTLDGDG-TLTNNQSGVKYRPNNQIGFYQSITADGNWGDEKL 251
           G ++MM  LR FS + PLY L  D  +L +   G   +PN +IG YQ++ ADG +    L
Sbjct: 201 GEQLMMGGLRSFSESSPLYALQADQQSLVSQVDGTVLKPNFEIGNYQAVDADGEFVGNAL 260

Query: 252 SPGYTVTTGWKNFTRVFTDEGIQKPFLAIFVWTVVFSLITVFLTVAVGMVLACLVQWEAL 311
           SPG+ V TGW NFTR+F D+GIQ PF+ IF+WTVVFS  +V  T+AVG+VLA +VQWE L
Sbjct: 261 SPGFVVNTGWDNFTRIFLDKGIQGPFIQIFIWTVVFSGGSVLFTLAVGLVLASVVQWEEL 320

Query: 312 RGKAVYRVLLILPYAVPSFISILIFKGLFNQSFGEINMMLSALFGVKPAWFSDPTTARTM 371
           +GKA+YR+LLILPYAVP+FISILIFKGLFNQSFGEIN  L+ALFGVK  WFSDP  A++M
Sbjct: 321 KGKAIYRMLLILPYAVPAFISILIFKGLFNQSFGEINGFLNALFGVKLKWFSDPYLAKSM 380

Query: 372 LIIVNTWLGYPYMMILCMGLLKAIPDDLYEASAMDGAGPFQNFFKITLPLLIKPLTPLMI 431
           L+I+NTWLGYPY+MILCMGLLK+IP DLYEASA+DGAGP  NFFKITLPL+IKPLTPL+I
Sbjct: 381 LLIINTWLGYPYVMILCMGLLKSIPSDLYEASAIDGAGPLDNFFKITLPLIIKPLTPLLI 440

Query: 432 ASFAFNFNNFVLIQLLTNGGPDRLGTTTPAGYTDLLVNYTYRIAFEGGGGQDFGLAAAIA 491
           ASFAFNFNNFVLI LLTNG PD +G++TPAG+TDLLV+YTYRIAFEGGGGQDFGLA+AIA
Sbjct: 441 ASFAFNFNNFVLIALLTNGAPDIIGSSTPAGHTDLLVSYTYRIAFEGGGGQDFGLASAIA 500

Query: 492 TLIFLLVGALAIVNLKATR 510
           TLIFL+VG LAI+NL+ ++
Sbjct: 501 TLIFLMVGVLAIINLRISK 519


Lambda     K      H
   0.324    0.140    0.429 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 761
Number of extensions: 33
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 514
Length of database: 523
Length adjustment: 35
Effective length of query: 479
Effective length of database: 488
Effective search space:   233752
Effective search space used:   233752
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory